MolNFT v1 · #72927 · protein

Crystal structure of apc complexed with asef

3NMZ · Apc variant protein: “Crystal structure of apc complexed with asef”. X-ray diffraction, 15 pockets (best druggability 0.80). MolNFT v1 #72927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NMZ
Type: protein
Length: 975 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apc variant protein; Rho guanine nucleotide exchange factor 4
UniProt: Q4LE70, Q9NR80
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 61% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apc variant protein	protein	406	71% helix, 0% strand	Q4LE70
B	Apc variant protein	protein	400	72% helix, 0% strand	Q4LE70
D	Rho guanine nucleotide exchange factor 4	protein	84	11% helix, 31% strand	Q9NR80
C	Rho guanine nucleotide exchange factor 4	protein	85	8% helix, 32% strand	Q9NR80

Pockets

15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	725	0.80	0.84	70	empty
2	587	0.77	0.84	78	empty
3	156	0.66	0.87	38	empty
4	87	0.65	0.91	22	empty
5	116	0.47	0.80	26	empty

Interfaces

4 interfaces between chains.

A–C · 1383 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 1336 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 927 Å² buried · 10 hydrogen bonds · protein-protein
D–C · 405 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3NMZ · Crystal structure of APC complexed with Asef · the same entry in another collection · chain A against A, TM-score 1.00
Q9NR80 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 4 (Q9NR80) · a predicted model of the same protein · chain D against A, TM-score 0.79

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q4LE70
Every structure of UniProt Q9NR80
Elsewhere: RCSB PDB 3NMZ · PDBe 3NMZ · UniProt Q4LE70 · UniProt Q9NR80

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